The death toll, and the way it's basically glossed over, is my biggest issue with the film. Superman felt anguish over his decision to defeat Zod - where was the similar anguish over the consequences of the battle which, while necessary, perhaps, was utterly devastating?
Other criticisms, like shaky cam, focusing on a unified character (rather than the secret identity angle) and "donning the suit not being epic enough" are simply stylistic choices. I guess ignoring the death toll is a style now, too (see: Avengers, Transformers, etc.) but for this film, which makes such a big deal about safeguarding and saving lives, ignoring the cost is, to me, a more relevant flaw in terms of the film's internal consistency.